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PECaller specifications


Unique identifier OMICS_19097
Name PECaller
Alternative name PEMapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes



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  • person_outline Stephen Warren <>
  • person_outline Michael Zwick <>
  • person_outline David Cutler <>

Publication for PECaller

PECaller in publications

PMCID: 5924597
PMID: 29091079
DOI: 10.1038/mi.2017.74

[…] sequencing. image processing and base calling was performed using standard illumina software. raw sequence reads were mapped relative to the human genome reference sequence (grch38/hg38) using the pemapper software tool (cutler dj et al, submitted) to identify single nucleotide variants (snvs)., nox1 variants were validated using sanger sequencing according to standard techniques., historic […]

PMCID: 5647121
PMID: 29025761
DOI: 10.1161/CIRCGENETICS.116.001690

[…] hudson alpha institute for biotechnology (huntsville, alabama) as part of the international 22q11.2 brain and behavior consortium to find genes for schizophrenia. variant calling was performed using pemapper software for read mapping to the hg38 (grch38) reference genome and pecaller software for variant calling. crossmap ( was used to convert genome coordinates […]

PMCID: 5414116
PMID: 28440315
DOI: 10.1038/ncomms15102

[…] array according to the manufacturer's protocol, and 100-bp paired-end sequencing was performed using an illumina hiseq 2000. raw sequencing reads were mapped to the whole mouse genome (mm10) using pemapper/pecaller ( with the default settings, and variant bases were annotated with seqant ( for samples subjected […]

PMCID: 4865318
PMID: 27009202
DOI: 10.1091/mbc.E15-09-0675

[…] version 3 with 100–base pair paired-end reads. raw data were returned to the eigc for bioinformatics analysis. raw reads were mapped against the c. elegans reference genome (ws190/ce6) with the pemapper software package. pemapper maps short reads to a reference genome by first decomposing those reads into k-mers (16-mers in this case) and then performing a hash-based “rough mapping” […]

PMCID: 3492087
PMID: 23020841
DOI: 10.1186/2040-2392-3-8

[…] analyzer ii (iga), raw base-calling data generated by iga were used as input for mapping and alignment. paired-end reads were mapped and variants were called relative to a reference sequence using pemapper (cutler dj et al., in revision). briefly, the pemapper is composed of four interconnected programs. the first program prepared a hashed index of the target sequence, the second program […]

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PECaller institution(s)
Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA; Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, USA; Division of Neurology, Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA; Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
PECaller funding source(s)
Supported by NIH/National Institute of Mental Health Grants U54 HD082015 and U01 MH101720, which are part of the International Consortium on Brain and Behavior in 22q11.2 Deletion Syndrome, and the Simons Foundation Autism Research Initiative.

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